sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / spearman.cpp

diff --git a/spearman.cpp b/spearman.cpp
index 72d5667e97a0e6a0a499464fe529699212ae8a91..49d5265259bc2ceb566d6f88f71fda30130b7945 100644 (file)
--- a/spearman.cpp
+++ b/spearman.cpp
@@ -10,6 +10,7 @@
 #include "spearman.h"
 
 /***********************************************************************/
+
 EstOutput Spearman::getValues(vector<SharedRAbundVector*> shared) {
        try {
                data.resize(1,0);
@@ -20,28 +21,51 @@ EstOutput Spearman::getValues(vector<SharedRAbundVector*> shared) {
                double sumRanks = 0.0;
                int numOTUS = shared[0]->getNumBins();
                
-               //calc the 2 denominators
-               for (int i = 0; i < shared[0]->getNumBins(); i++) { 
+               vector<double> rankVectorA(savA.getMaxRank()+1, 0);
+               int currentRankA = 0;
+               for(int i=savA.getMaxRank();i>0;i--){   
+                       int numWithAbundanceI = savA.get(i);
+
+                       if(numWithAbundanceI > 1){      rankVectorA[i] = (currentRankA + 1 + currentRankA + numWithAbundanceI) / 2.0;   }
+                       else                                    {       rankVectorA[i] = currentRankA+numWithAbundanceI;        }
+                       currentRankA += numWithAbundanceI;
+               }
+               rankVectorA[0] = (numOTUS + currentRankA + 1) / 2.0;
+               
+               
+               vector<double> rankVectorB(savB.getMaxRank()+1, 0);
+               int currentRankB = 0;
+               for(int i=savB.getMaxRank();i>0;i--){   
+                       int numWithAbundanceI = savB.get(i);
                        
+                       if(numWithAbundanceI > 1){      rankVectorB[i] = (currentRankB + 1 + currentRankB + numWithAbundanceI) / 2.0;   }
+                       else                                    {       rankVectorB[i] = currentRankB+numWithAbundanceI;        }
+                       currentRankB += numWithAbundanceI;
+               }
+               rankVectorB[0] = (numOTUS + currentRankB + 1) / 2.0;
+               
+               
+
+               for (int i = 0; i < shared[0]->getNumBins(); i++) { 
                        int Aij = shared[0]->getAbundance(i);
                        int Bij = shared[1]->getAbundance(i);
                        
-                       int rankA = savA.get(Aij);
-                       int rankB = savB.get(Bij);
+                       float rankA = rankVectorA[Aij];
+                       float rankB = rankVectorB[Bij];
                        
                        sumRanks += ((rankA - rankB) * (rankA - rankB));
                }
-               
-               data[0] = 1.0 - ((6 * sumRanks) / (float) (numOTUS * (numOTUS-1)));
+               data[0] = 1.0 - ((6 * sumRanks) / (float) (numOTUS * ((numOTUS*numOTUS)-1)));
                
                if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
                
                return data;
        }
        catch(exception& e) {
-               m->errorOut(e, "Soergel", "getValues");
+               m->errorOut(e, "Spearman", "getValues");
                exit(1);
        }
 }
+
 /***********************************************************************/